Q. Thank you, same here. You know, you did miss
Ken Miller's testimony which Mr. Rothschild referenced, and it
was quite a show, but let me ask you this. I learned something
from Dr. Miller's testimony that I didn't know before, which is
that Ken Miller believes that God is the creator of all things
seen and unseen, and I ask you this. That doesn't make Ken Miller
an intelligent design creationist, does it?

A. I'm sorry that I didn't get to hear Ken
himself. I feel like one follows dogs and children, you know, you
don't want to do that. You also don't want to follow Ken Miller.
He's a hard act to follow. And I don't know the way in which he
put that, so could you say again what that --

Q. My request is this. Does Dr. Ken Miller's
belief that God created all things seen and unseen make him an
intelligent design creationist?

Q. Okay, and that's because the religious beliefs
of a given person doesn't determine whether or not that person is
engaged in science, is that correct?

A. This express belief in a creator is compatible
with evolution, and so that he believes that or that another one
doesn't is not substantive to that.

Q. In fact, I believe some people describe that
position as theistic evolution, the notion that evolutionary
theory is consistent with their religious faith, is that
correct?

A. That's right. Theistic evolution is sometimes
used inconsistently though. Occasionally it is used in the
literature to refer to a creationist type belief. That
distinction I think is better, the term that's is better used is
evolutionary creationism in that case. So sometimes theistic
evolution is misused in that way, but the way that you're using
it and the way in which you've described it is correct,
compatibilist view.

Q. And that's because a theory doesn't become
scientific or not scientific based on whether persons discuss
whether it's consistent with a given set of religious beliefs, is
that correct?

A. The way in which one holds a position,
articulates a position is relevant. So you have to look at
exactly what they say. Sometimes people will make and hold a
theistic view and claim that it's science. Other times you will
speak of it as separate. So you have to look specifically at what
people say with regards to that.

Q. But a theory doesn't become scientific or not
scientific based upon whether its proponents have discussed its
consistency with religious beliefs, is that correct?

A. When a person discusses whether or not the
content of a view is consistent or not, right, at that point one
is, it should be clear as to whether one is speaking qua
scientists or qua philosophers say, and as long as one is clear
about that then that's quite fine. One should not say qua
scientist that this is so or not theologically.

Q. Well, is it your testimony here today that as
theory becomes scientific or not scientific depending on whether
a proponent has discussed its consistency with religious
beliefs?

A. To determine whether a theory is scientific or
not you have to look at the content of that theory itself.

A. So the proponents of that theory would be what
they've said is going to be relevant when you find out about what
that theory exactly says.

Q. And forgive me for interrupting you. Is it your
opinion that a theory can become non-scientific because a
proponent has discussed its consistency with religious
beliefs?

A. Again my point has to do with what people say
substantively. So it depends on what they say when they discuss
its consistency. If they discuss substantively theological
content, then that's part of the content of the view, then that
is relevant.

MR. GILLEN: If I may, Your Honor, I'd like to ask
the witness to examine his deposition testimony.

Q. Thank you. Dr. Pennock, I have given you copy
of your deposition which I took on Tuesday June 14th, 2005, and
I'd ask you to look at page 51 of your deposition testimony, line
10. Have you had a chance to --

Q. Okay. If you look at page 50, on page 9 I asked
you a question, "Concretely do you think that a theory would be
properly classified as not scientific if a proponent of that
theory discussed its metaphysical implications?" And you asked me
to ask that question again, and then you gave an answer. Would
you look that answer over?

Q. I ask you again today, is it your opinion that
theory becomes scientific or not scientific based on whether
someone has discussed whether the theory is consistent with
religious beliefs?

A. And as I said there, if the discussion is
merely is it consistent or not, that by itself does not make it
so.

Q. Okay. For example, the Big Bang theory is not a
non-scientific theory, even though it's consistent with some
people's belief in creation out of nothing, is that correct?

A. As a scientific theory the Big Bang itself is
not a religious view, that's right.

Q. Dr. Miller also noted that he had a friendship
with Richard Dawkins, and it was brought to his attention that
Richard Dawkins in his book "The Blind Watchmaker" had made the
assertion that Darwin made it possible to be an intellectually
fulfilled atheist. My question to you is it's true that Dawkins'
observation along those lines doesn't mean that evolutionary
theory is a religious theory, is that correct?

Q. And he's engaged in what's sometimes called
metaphysical extrapolation, is that correct?

A. I don't see in that statement that he's giving
metaphysical extrapolation. The quote that you have is one that's
commonly quoted, makes it possible to be an intellectual
fulfilled atheist, so that's simply saying something about his
own comfort.

Q. And Dawkins' observation doesn't make evolution
a non-scientific theory?

A. That's right. He's not saying that this is
something that is part of the contents of the theory at all.

Q. And that assertion on Richard Dawkins' part is
not a scientific assertion?

A. The assertion there is not saying something
about the content of the view qua scientist, that's right.

Q. And when you look at Dawkins' statement, it
makes it very evident that not everything that comes out of a
scientist's mouth is science, correct?

A. That's correct. Sometimes people will speak qua
scientist and sometimes they will speak about something from
their own personal views.

Q. Now, Ken Miller is a friend with Richard
Dawkins, who engaged in this, who made this statement, and Ken
Miller as I have told you has testified here in court that he
believes God created all things seen and unseen. That association
between Miller and Dawkins doesn't make evolution a
non-scientific theory, correct?

A. No, I think one should be friendly as possible
with people of all beliefs.

Q. Sure. And the fact that one of Dr. Miller's
friends has engaged in a non-scientific statement about his view
concerning the possible implications of evolutionary theory
doesn't mean that Ken Miller isn't engaged in science,
correct?

A. The fact that he's referring to conversations
you're saying with Dawkins? No.

Q. No. Connections of a given individual who
proposes a given theory with a religious organization don't make
a scientific theory non-scientific, do they?

A. Unless it's something where the theory is,
includes the content of this, but the mere association does
not.

Q. So, for example, Ken Miller indicated to the
court that he's a Roman Catholic. That doesn't mean because he's
affiliated with the Catholic Church that evolutionary theory is a
non-scientific theory, correct?

A. That's right. What one looks to is the
statements about the theory itself. What is its substantive
comment. So my commence here with regard to intelligent design
had to do with the contents of view, statements like that of
Nancy Pearcey, who says that what intelligent design allows one
to do is in her view sit in what you call it the
supernaturalist's chair. You can sit in the naturalist's chair.
She said the design theory lets, demonstrates that the Christian
can sit in the supernaturalist's chair, and she says it lets one
in one's professional life see the cosmos through the lens of a
comprehensive biblical world view. So that's content of the
theory, the content of what design is. But that's different from
whether one is a member of a particular church or something.

Q. And I understand that Nancy Pearcey is entitled
to her opinion as to what the benefits of intelligent design
theory are, just as Richard Dawkins is entitled to his opinion
concerning the benefits of evolutionary theory. But that's their
opinion, correct?

A. The difference there is that Nancy Pearcey, as
one of the authors of "Pandas," and describing in this case, this
is in her later book "Total Truth" where she's saying here's what
intelligent design is, it's something that demonstrates the
objective truth of Christianity, restores it to genuine
knowledge, she's telling us something about the content of
intelligent design, as a leader of the movement describing its
substance.

Q. So but Richard Dawkins is not a leader of the
evolutionary movement?

A. He's a scientist. It's hard to think of the
evolutionary movement as just a bunch of scientists who are
investigating the world.

Q. Sure. Well, a lot of intelligent design people
think that it's hard to think of an intelligent design
movement.

A. They explicitly talk about their movement.
That's actually language they use very often.

Q. Are you familiar with evolutionary theory being
discussed as a big tent theory?

Q. It's also true though that scientific progress
has been made prior to, what shall we say, what we think of as
modern science, isn't that correct?

A. If you're saying in terms of whether we made
scientific discoveries, things that we would regard as empirical
discoveries of that nature before the scientific revolution,
certainly so, my examples from Hippocrates and others that comes
before that period, but we still sort of recognize that as the
making use of methodological naturalism.

Q. So scientific progress has been made before
what we characterize as modern science with its commitment to
methodological naturalism, isn't that correct, Dr. Pennock?

A. As I tried to say, the term methodological
naturalism is one of these philosophical long terms that
scientists themselves may never have heard of. So the important
thing is whether in their practice, in their method they're
actually following it or not, and what I was trying to explain is
that this notion that we're identifying now with methodological
naturalism in fact can be found in an early form even in the
early Greeks. So I wouldn't say that it's sort of before science.
In that sense they are sort of performing what we would now think
of as science to the extent that they're making use of that
method.

Q. Let me ask you this. I mean, things such as
gravity, that was once thought of as an occult force,
correct?

A. Exactly. This was something where it was
actually sometimes described as spooky action at a distance, and
the change that happened there was to reconceptualize it as a
natural property, see it as something that was a law of nature in
the same way that other laws are, and to treat it as something to
be experimented upon, investigated in the normal ways, under the
normal constraints of methodological naturalism, and essentially
what that does is take it out of the realm of the occult and see
it as a natural sort of thing.

Q. Right, and that's what Newton did. He I believe
the term that you used which is useful is explicate. He
explicated. Is that correct. or am I misunderstanding?

A. Explication is what philosophers do in trying
to take a notion, a concept in its form within a practice and to
try to make it systematic and rigorous. So Newton himself would
not be doing explication. Newton is doing research as a
scientist. Newton is one of those transitional figures where we
now of course cite him for the scientific work, but we also leave
aside those aspects that were unscientific.

Q. And the result of his work was to take a force
previously thought to be occult and I believe as you have
testified to bring it into the natural world, the natural causal
world, is that correct?

A. That's to say what he did was treat something
under the constraints of methodological naturalism to say we'll
view this and see it no longer as supernatural, no longer as
breaking the laws of nature, but actually as a law of nature
itself.

Q. Isn't it true that in his day Newton was
thought to have departed from naturalism?

Q. Isn't it true in his day Newton was thought to
have departed from the law of naturalism?

A. As I said, this is something where Newton
himself is a transitional figure, and I don't know if something
specific in that day where there was a discussion with regard to
that. Newton himself was very straightforward that in his rules
of reasoning he says we shouldn't introduce superfluous causes.
He talks about explaining things in terms of philosophy by which
he means natural philosophy or what he calls now science rather
than bringing in the divine. So with regard to his scientific
work we now take his scientific work, I don't think there's a
departure from methodological naturalism.

A. Leibniz and Newton were at loggerheads as for a
number of reasons. Each thought that they were the origin, the
originator of the calculus or fluctions, and so they were not
friends with regard to things. Certainly that's right, Leibniz
criticized some of Newton's arguments on a number of points.

Q. And you're aware of the hypothesis that
intelligence is an emergent property of matter, correct?

A. That would be viewing intelligence in the
ordinary science, scientific sense, under the constraints of
methodological naturalism and treating it like any other
property.

A. If viewed in that way, then that would be an
example of design understood, as I was trying to give examples of
the way archaeologists use it, it's treating it in the ordinary
sense the natural sense of design. Someone, some person like us
did something.

Q. Isn't it true that as we sit here today
scientists are investigating what some people call psychic
powers?

A. I know that there are a few scientists who did
that I believe. Mack is one name, someone who's done this. So
there are a few scientists who have done that, that's right, and
what they do in that case is really the same thing. It's often
misunderstood to think, to call something paranormal means that
it is supernatural. Essentially what's going on in those
scientific investigations is to say no, that's not so. We will
again treat this purported phenomenon, ESP or telekinesis for
example, as though this is a natural, still yet unknown, but
ordinary causal process, treating it essentially in the same way
we treat other things under the constraints of methodological
naturalism, reconceptualizing it as a natural thing rather than a
supernatural.

Q. And that's more or less what Newton did, right?
He took something that was occult or not normal and he studied it
and brought it from the supernatural or paranormal to the natural
world by virtue of his theory, correct?

A. It's a little misleading to say he took it from
supernatural and brought it in. I mean, essentially what is going
on is reconceiving something that we thought was supernatural we
now realize isn't. That's different from making a claim this is
the supernatural. That's departing, that would be to depart from
methodological naturalism.

Q. Let me ask you this. There are scientists
investigating as you said telekinetic powers. Those scientists
perform experiments, don't they?

A. I know of some experiments related to attempts
to study this. It's always a question as to whether in fact it's
a real phenomenon, but there are some attempts to do that, and
again it's done by treating it as though it is a natural
phenomenon.

Q. Isn't it true that Fodor argues that mind
cannot be explained in terms of evolutionary naturalism?

A. I don't know Fodor's work specifically with
regard to that point. If you could say a little bit something
where he's coming from on that.

Q. No, if you don't know that's fine. How about
Saul Kripke, isn't it true that Saul Kripke argues that mind
cannot be explained by evolutionary naturalism? Are you familiar
with his work?

A. Again I don't know any specific thing where
he's claiming that this is something that departs from
science.

Q. Isn't it true that Fodor argues that scientists
have failed to establish clear physical criteria for saying that
someone is in a particular mental state?

A. That's a claim that I do know that Fodor has
made. It has to do with establishing the direct connections
between these. It's not something that departs from the rules of
science. It simply says here's an unanswered question, we don't
yet have an answer from that.

Q. And isn't it true that Kripke likewise argues
that scientists have failed to establish clear physical criteria
for identifying a particular mental state?

A. Yes. Kripke is writing quite a few decades
back, and again the same point is true, science is quite clear we
have not yet been able to do this. There are lots of those open
questions where we don't have an answer to it, but that's
something I would agree with as well. We don't yet have an answer
to that.

A. Mendel is important as we think of as the
founder of genetics. It was Mendel who was the investigator of
factors that determine traits. He was working with peas, beans,
and postulated factors which would produce the patterns that were
seen in differential colors for example in peas or short and long
stem lengths. So Mendel 's laws we speak of have to do with basic
features of the genetic mechanism.

Q. And isn't it true that Mendel's paper on
genetic theory was rejected for publication by the German
botanist Karl Von Nageli , if that's the proper pronouncing,
which I doubt. It's spelled N-A-G-E-L-I. Isn't that true?

A. I don't know about that. It was eventually
published in a regular scientific journal.

Q. And Mendel's theory was lost for forty years
between the time he submitted it for publication initially and
the time it was, his work was rediscovered, correct?

A. Right. This was one of the examples where
science re-finds something that had been known before those
genetic laws were rediscovered independently three times by
scientists essentially at the same time who then all looked back
into the literature and found Mendel's work and gave him credit
for that.

Q. Now, Von Nageli, the man who rejected Mendel's
article for publication, did so because Mendel was an
anti-evolutionist, correct?

A. I'd be surprised if an editor would tell
somebody that it's rejected because they're an evolutionist in
particular because at that point this is the same time that
Darwin's work is getting underway. So those things had not yet
even come together. I don't know the details of this. If there's
a letter to that effect I'd be interesting in seeing it.

Q. And modern genetics is one of mainstays of the
so-called neo-Darwinian synthesis, correct?

A. Part of what Mendel's work did was show how it
is that the genetic mechanism works in early form. Obviously
we've learned much more since then, so we don't talk about
Mendel's theory when we're talking about genetics except as sort
of a tip of the hat to a progenitor. And so yes, we think of
Mendel as the founder of that.

Q. Dr. Pennock, isn't it true that there's not
agreement among philosophers of science concerning the validity
of methodological naturalism?

A. The term methodological naturalism is fairly
straightforward in the literature. There have been criticisms of
it from people like Del Ratzsch from discussions specifically of
this debate. So there's some who have taken up a sympathetic
position to the intelligent design folks and tried to argue that
we could dispense with this.

A. I don't think of it as a dispute. He's actually
dispositive with regard to, pretty much with regard to the
article, with regard to the book.

Q. Is it your opinion that Dell Ratzsch is an
intelligent design creationist?

A. Ratzsch himself, I don't know his position on
this. I haven't talked with him in regard to that.

Q. Isn't it true that initially some scientists
resisted the Big Bang because of its consistency with Christian
religious beliefs?

A. Some people rejected it because of its
connection to Christian religious beliefs? I know that there were
those such as Eddington, who was one of the early scientists to
look at this and investigate it scientifically, that he had
troubles with it philosophically. It's hard to say that he did
because he was, I'm not sure how you put it, because of its
agreement with Christian beliefs.

Q. In fact, Einstein tinkered with his equations
to avoid tailoring his equations and his theory to the reality of
an expanding universe, correct?

A. When you say tinkered with, what he was doing
was taking into account what was known and trying to work into
his general theory. He was attempting to come up with a very
general view, a constant, a cosmological constant to make the
equations work, make them fit with the evidence.

Q. It's evident today that you published two books
that have to do what you call intelligent design creationism. I
trust you have no objection to your books being in the library of
Dover High School?

A. I actually had someone call me and offer to
donate sixty copies to the library, and my reply was I'd be happy
for him to do that, but I thought that he should really include
sixty different books, which would be easy to come by, and happy
that mine would be amongst them. I should have just taken him up
on the offer though.

Q. You're familiar with the French chemist
Lavoisier? Did I say that correctly?

Q. By that he meant a reinterpretation of
knowledge in that area as it had been known to that time,
correct?

A. This is something within the discipline of
chemistry that would have been regarded as a significant change
in basic assumptions. So that's right, it's not something that
was a challenge to science itself. It was a challenge to some
specific chemical presuppositions.

Q. When you say challenge to science itself, you
mean science as characterized by a commitment to methodologi cal
naturalism?

A. That's right. There's nothing in Lavoisier's
revolution, the chemical revolution, that was at all a challenge
to the basic methods of science.

Q. And that consisted in a radical re-thinking of
theory of universe, shifting it from a geocentric theory to a
heliocentric theory, correct?

A. That's right. Historians now more credit Kepler
with that and talk we should say, we should really say it's a
Keplerian revolution because it was Kepler who was more detailed
in being able to establish the laws, orbital laws and so on and
how those work, but yes, we do credit Copernicus as well with
shifting our perspective with regard to is center. Again neither
of those is a change in the methods of science itself. It's
accepting those and giving a different physical account of the
world.

Q. And again when you say that, you mean it
doesn't pose a challenge to the convention of methodological
naturalism, correct?

Q. Your claim concerning these views that
intelligent design focuses on natural selection is based on, and
that's not an accurate characterization of the intelligent design
position, is based on your opinion concerning who belongs in the
intelligent design camp, correct?

A. What I have done throughout my research is to
read the full range of proponents, focusing most upon the key
leaders of the movement, but also more broadly and understand
them in their own terms, the way in which the literature, the
intelligent design literature is presented.

Q. And I do understand that you have conducted
research, but that research provides the basis for the opinion
you have offered here today, correct?

A. Behe has said a number of things with regard to
common descent. In his book, in fact he's usually described as
someone who accepts it, but when you look specifically at what he
said, he's always very careful in his wording and says thing like
"I have no particular reason to doubt it," something of that
sort, leaving himself a little bit of wiggle room with regard to
whether he actually accepts it or not or is just agnostic with
regard to it.

A. I know what he has said, and he has said, "I
have no particular reason to reject it."

Q. I want to ask you a few questions about your
work in the computer science area and Evita. You testified that
in your opinion that Evita is an artificial life system designed
to test evolutionary hypotheses, correct?

Q. And you said today and I believe in your
opinion that it's designed to instantiate Darwin's law,
correct?

A. That's correct. By instantiate, just so that I
this kind of explain this sort of philosophical term, the
difference here is between a simulation of something and an
actual instance of it. That's to say a realization of it. In the
Evita system we're not simulating evolution. Evolution is
actually happening. It's the very mechanisms of evolution itself
as Darwin discovered them. The organisms actually do self
replicate. They do randomly vary the code changes. The mutations
happen at random. There is competition and actual natural
selection. So these are not being simulated. Those processes are
actually happening. So that's the sense in which it's an instance
of evolution, not just a simulation.

Q. And to make sure I understand, it seems you're
saying that the instantiation makes it a more perfect model of
Darwinian law of natural selection, is that correct?

A. What I'm saying is it's an actual example of
it, that what we have in the system our organisms, Evitians, have
the very properties that the Darwinian mechanism discusses. So
it's not a simulation of replication. They are actually self
replicating. It's not a simulation of a random mutation. That's
what's going on with the code. It's not a simulation of natural
selection. They do compete and are naturally selected, without
intervention, without design.

Q. And Mr. Rothschild asked you and I believe you
testified that the program doesn't address the question of
origins, but rather the process of Darwin's law, it's working out
in the computer program organisms, correct?

A. It doesn't deal with the origins of life. It
deals with the evolution of complexity of adaptations. So origins
can sometimes be used in both ways. So what's relevant here is
it's not about the origin of life. It's about the origin of
complex traits.

Q. And I believe you said that the overall purpose
of the project is to test how evolution actually works, is that
correct?

A. That's right. What we're able to do in the
system is put forward an evolutionary hypothesis and then set up
a controlled experiment and let the system evolve with
replications, as many are as needed, and in some cases you might
have fifty different populations replicating in a controlled
situation, fifty in an experimental situation, so that you can
then watch what happens in each case and observe evolution, the
Darwinian process, do its stuff.

Q. Now, if someone looked at a computer program, I
think you have said that it was written by a particular
individual called the, what did you call it, the genesis program
or the --

Q. Ancestor program, forgive me. They would look
at that and immediately know that was done by a computer
programmer, correct?

A. Not necessarily at all. In fact, one can look
at these things and not know which things were coded by a
programmer and which things were evolved. We know because we put
them in there this was the one that we coded, but if one were to
just look at them, you wouldn't necessarily be able to tell at
all.

Q. So is it your testimony that if someone
happened to cross that computer program, they wouldn't know that
someone had designed it?

A. That's right. You would not be able to pick out
the ones that were evolved from those that Charles Ofria hand
coded as the Ancestor. As I said, what the Ancestor does is
simply replicate it. It's a very basic program. Most of it is
just blank code, and as the organisms evolve it can actually turn
out that they lose the ability to replicate. Some mutations are
harmful.

Many are. Most are, or neutral. It might make no
difference. Some mutations can actually make them better
replicators, and if it turns out that random mutations replicates
better than another organism, that means that in the competition,
in the digital environment, those will be naturally selected. So
what you'll have over time is the evolution of for example faster
replicators. That is they figure out a way to replicate faster
than the original programmer programmed in.

Or it could turn out that they'll be worse, and
those will then lose out in the competition. So what you see is
the evolutionary process, random mutations to the code, being
naturally selected for and generation after generation organisms
evolving, in this case better replication ability. Or, and this
is the other thing that's characteristic about Evita, it can
evolve the ability to perform complex logical operations, and in
this case again it's not something that was programmed in at
all.

The original Ancestor could do none of that, but
what one sees at the end are organisms that have evolved these
complex abilities. The code has changed. It's acquired an ability
that it did not have before. And that's what we're able to see,
something we know that was designed at the beginning but couldn't
do any of this stuff to something at the end that has evolved so
it's quite complex.

The set of instructions has to be executed in a
specific order to produce a particular function. That's something
we can look at and say how did it do it, and often they're very
clever, they evolve things where the programmer would think why,
I would never have thought even to do it that way. And that's
what allows this to be a nice model for examining how evolution
can produce complex functional adaptations.

A. If you have it, and the other thing about it is
-- sorry, I get excited about this. We can trace, we can keep
track of the full evolutionary history. So we have a complete
fossil record if you will. So after we've see that it's evolved
something we can look back and look, it's a mutation by random
mutation of how that evolved.

Q. Sure, and forgive me if my question was
imprecise. I didn't want to cut you off, but my question is a
little different than one you've answered at least as I see it,
not technical, which is this. I'm not asking about the difference
between the organisms you're looking at. I'm saying if someone
came across that computer program, the Ancestor program, wouldn't
they believe it was designed?

A. And my answer is that you really can't say
that. You might believe it and you'd be wrong. You can't tell the
difference between the one that was encoded and one that was
evolved later on.

Q. So it's your testimony that someone could
believe the computer program was not designed?

A. You're asking a psychological question about
what someone could believe, is that right? In that case they
could believe all sorts of things, but the question has to do
with can you look at them and tell this was one that was
designed, and the answer there is no, not necessarily.

Q. Let's use your definition and let's constrict
causality to the natural world and I'll ask you the question
again. If someone like myself wandered down to Michigan State
University and came across your computer system generating this
pattern that you have described in great detail which is designed
to substantiate Darwinian mechanism, is it your testimony or do
you have an opinion concerning whether someone like me would
think that was designed or not?

A. Someone might think it was. You might look at
it and you might say wow, that looks pretty complicated, how
could that have happened. You might think this is so amazingly
functional and interrelated, it's irreducibly complex, it had to
have been designed by someone, and you'd be wrong.

Q. So I would be wrong if I inferred that that
computer program has been designed by a computer programmer?

A. That's right. You'd be wrong about that. The
ones that emerged at the end of the evolutionary process have
specific code that lets them do specific adaptive functions, and
that was not programmed in.

Q. Would I be wrong if I inferred that the
computer program had been created by a supernatural force?

A. If you were to conclude this just as a
theological position or as a scientific position?

A. So again, and this is a nice example to sort of
show the difference between thinking about this as a scientist
under methodological naturalism versus the intelligent design
notion of opening our minds to the possibility, what I have said
here is that the organisms at the end weren't designed. We didn't
have a hand in doing that. They evolved. Someone who says well,
we have to consider the possibility of supernatural interventions
might say well, you know, God was in there or some supernatural
designer was in there changing the bits inside the computer.

Well, you know, we don't know if that's true, and
no scientist can ever know if that's true. That's not a testable
proposition. So in that sense we can never rule that out. That's
part of what it means to be a methodological naturalist. So we're
neutral with regard to that. Our conclusion that there was no
design is one based upon methodological naturalism, namely we're
assuming that this is working through ordinary laws, that there
aren't any interventions that breaking laws. We know that we
didn't do it, and that's what we can say as scientists. If God or
some supernatural being is in there fiddling with the gates, the
logic gates such that there really was design, we don't have any
way of testing that.

Q. Dr. Pennock, you testified that if someone were
to reject, if the intelligent design theorists or intelligent
design creationists as you call them were to succeed, modern
science would be knocked backward. Is that your testimony
today?

A. That's right. It would be a return to this
earlier pre-scientific notion.

A. Yes, Larry Laudan was a philosopher of science
who actually has been a previous professor at the university
where I did my work.

Q. And Larry Laudan said he believes that
creationism is science, it's just bad science, correct?

A. You're referring to a particular article that
Laudan wrote that Michael Ruse included in his anthology on
creation science movement in the early 80's, and in that case
Laudan is making arguments that creation science should be
allowed to be science in that he says it's offering a claim that
could be proved, but that is found to be false such as the age of
the earth, because we know that that's not true. So in that sense
he says this is something that is bad science.

If one were to put that forward as though it were
science, that would be wrong, it's bad science. But he said we
can allow that as science. Now, he does that under the assumption
that we're judging this under the kinds of rules that I'm
mentioning, to say that we're judging that the young earth
hypothesis, let's say that the earth is ten thousand years old is
false, and that we have disconfirmed that. That disconfirmation
is done by assuming that we can judge it under the rule of
methodological naturalism.

That's to say that we're taking our ordinary
notion and not allowing supernatural intervention. If we were to
allow it, then we would not be able to say that this is something
that has been disconfirmed. That's to say if you take seriously
the content that departs from scientific method and at that part,
point, you'd be wrong to say that it's just bad science. At that
point you'd just say it's not science.

So this is always the sort of a subtle point
that's important to try to get across, and let me try to put it
this way, right? It's often complained by creationists that they
say oh, you know, you're saying that we can't be falsified, and
yet at the same time you're saying that we are falsified. Gosh,
isn't that a contradiction? And that's just a misunderstanding,
right?

The claim that it can't be falsified is the claim
that it can't be falsified if one is departing from
methodological naturalism. That is to say if you treat this as
just an ordinary scientific hypothesis, then you'd say well, we
projected that the earth is ten thousand years old. But if you
depart from it and take seriously the supernatural content, then
you can't say that anymore, because at that point who knows?

Young earth creationists, some of them have said
well, the world looks old, but it looks old because God made it
old, that really it is six thousand years old but he made it so
that it appears to be much longer, did much, much earlier. Well,
that's sort of a deceptive view about the way things were
created. But if you take that view that it's possible to say that
the supernatural being is deceiving us in this way, then there's
no way to say that we've disconfirmed that.

For all we know the world may have been created
five minutes ago and we've just been implanted with memories to
make us think it that it's much longer, right? There's no way to
disprove that. If you seriously take the supernatural
possibility, then you can't disconfirm it. So that's the sense in
which it's important to say under the assumption of
methodological naturalism, we have disconfirmed it, it's bad
science, that's what Laudan is talking about, but if you were to
take seriously the non-natural part, that's to say rejecting
scientific method, then it's just not science, and we can't say
that we have rejected it. So there's always these two different
hypotheses. You've got to keep them distinct. There's no
contradiction.

Q. Hello again, Dr. Pennock. Early in your cross
examination Mr. Gillen brought up the subject of Newton and
suggested that there have been supernatural explanations for
action at a distance, I think you called it spooky action at a
distance, but that Newton took that supernatural proposition and
came up with a natural explanation, is that correct?

A. That's right. Essentially it's a
reconceptualization of what was taken to be supernatural and
saying oh, no, it's not really supernatural, we're not even going
to think of it in that way, we'll think of it under the
constraints of methodological naturalism and treat it as a
natural hypothesis and then treat it as such.

Q. And your example of epilepsy with Hippocrates,
a similar phenomenon, we had a supernatural or spiritual
explanation and Hippocrates said no we can come up with a natural
explanation?

A. Exactly. And again one remains neutral
metaphysically about whether or not there is some divine basis
for this. That's just something that's outside of science. It's
what one is doing within science as saying this is just a natural
explanation, that's what we’re getting.

A. Explicitly not. Their basic goal and
proposition is to change the ground rules. They want the
supernatural to be introduced as you know Nancy Pearcey has said,
this lets us as professionals, intelligent design demonstrates
that Christians as professionals can sit in the supernaturalist's
chair. She's not saying that we can say what we thought was
supernatural is natural. No, this is meant to be substantive,
it's meant to be a rejection of the basis of science.

Q. Dr. Pennock, isn't intelligent design in fact
doing the exact opposite as Newton, taking a natural phenomenon
for which we have natural explanation and arguing that we have to
replace it with a supernatural explanation?

A. Exactly, in the sense that the kinds of
examples that they give of design inferences, every single one of
them is a natural notion of design. No one has any objection to
those, but those are done under ordinary constraints within
science, and we can give evidence and test those, which we do all
the time. They're wanting to reject that notion such that even
ordinary cases wind up being quite extraordinary.

Q. And in the case of the theory of evolution we
have a natural explanation?

Q. Dr. Pennock, it's your opinion that we have a
natural explanation for the origin of life?

A. I haven't said something about the origin of
life. I think science does not yet have an explanation of the
origin of life. It's a topic of research. People are working on
it. One of my colleagues at Lyman Briggs is part of a project
that is actually looking at a new method for how one can have an
explanation of that. We'll see whether that pans out or not. So
there's real research going on, but that's not part of the
Darwinian theory. Darwin has set aside that question. The
question is the origin of species, the origin of adaptations, of
complexity and so on, and that's where we can say we have an
explanation.

Q. Do you have an understanding concerning whether
intelligent design theory as I call it, intelligent design
creationism, is usually what speaks to the origin of life?

A. In some of their literature they have used
origin of life explicitly as an example of something that cannot
be explained naturally. Stephen Meyer for example often uses that
in his talks. Others have as well. Sometimes though the focus is
on things other than the origin of life.

Q. And there are philosophers of science who
believe that mind cannot be understood in terms of evolutionary
naturalism, correct?

A. The question is whether science has been able
to explain this in natural terms.

Q. No, the question is whether there are
philosophers of science who believe that mind cannot be explained
in terms of evolutionary naturalism.

A. If we're talking about philosophers, then
that's certainly true. There are some philosophers who will
consider the matrix hypothesis as well that life was created five
minutes ago. So yes, indeed, we have lots of discussions about
that within philosophy.

MR. WALCZAK: He will be here at 1:15. The
reporters will be here with them, and I advised him that Your
Honor would give him an opportunity to make whatever arguments he
wants to make at that time, and at that time we'd go from
there.

THE COURT: Well, my intention would be to meet in
chambers with all counsel, not the reporters, and then have a
discussion and see precisely where we are. I think there's it's
appropriate for you not to try to paraphrase what Mr. Benn's
exact position is.

THE COURT: All right. Why don't we do that then.
Let's break and we'll come back roughly, why don't you assemble
in chambers. I’ll let you all find Mr. Benn when he gets
here and yank him into chambers and we'll have that discussion,
and then my intention is if in fact the answer is in the
negative, I guess we're going to have to have a proceeding in
open court with respect to the reporters to see where that goes
at this point. You do not know whether it's his intention at this
point, you don't know the reporters' intentions with respect to
whether they would indicated that they'd testify? That seems
rather counterintuitive.

MR. HARVEY: Your Honor, I want to give you a heads
up on something else that's coming up this afternoon. Probably
not at momentous as this. This afternoon we're going to call
Steve Stough, who read a number of the -- he only knows what he
read in the paper, and so we're going to do again what we did
yesterday, which is attempt to introduce the article.

MR. HARVEY: The purpose of Mr. Stough is to
testify about the harm to him, his perception of the Dover school
district's public statement that was published, but also to
testify about what he learned through the paper at the time,
because we think it's relevant to the effect on the community and
the endorsement test.

THE COURT: Well, they have an objection, and I
haven't ruled on whether or not the contents of the papers are
admissible for the purpose of the effect portion, and you're
forewarned that I might not allow that. You know, that compels me
to decide that objection, and if I have to do it this afternoon I
may not allow it as it goes to --

THE COURT: Your argument is that it's not clearly
for that purpose, and I understand that argument. I think this is
a complicated question and, you know, we'll rule as we must if
you bring him in at that point. I think it's difficult, you know,
I've made the popular analogy to unringing the bell, I think in a
bench trial intellectually I can separate out one from the other,
but I'm not so sure I should, and I think that's entirely
problematic

Now, you know, if I would not allow that testimony
for example, and if for example the determination that I have
made with respect to reporters is appealed to the Third Circuit
and if the Third Circuit believes that I'm correct, and if the
reporters are compelled to testify, and if you get the newspaper
articles in through that mechanism, then that I guess would allow
you conceivably if I sustain an objection this afternoon to bring
this witness back in a rebuttal phase, and I wouldn't prevent you
from doing that, but at this stage I have to tell you I don't
think it's clear as you believe it to be that I should simply let
the newspaper article in on the effect.

And I have to tell you, too, that given the state
of jurisprudence on these issues, which is somewhat dicey, and
all of you would admit that probably in moments of candor, that
to simply state that you introduce it on the effect part of it
and it doesn't go to truth I think is problematic, because I
think it does wash over the truth, and I think courts are unclear
on that point, and I might say that also to further buttress the
difficulty you have.

MR. HARVEY: Let me, Judge, just have a couple of
other things I think you need to know. One is is that I
anticipated that if when I did this with the articles today that
you might take it under advisement until later if the reporter
issue hadn't been considered, just as we did yesterday, and I was
putting a heads up, just I didn't want you to think I was butting
heads with you.

THE COURT: No, and to be fair I understand that
and I respect that. But you understand it wouldn't be so much
that I take it under advisement. It might be that I would sustain
the objection, and then you're left with the scenario that I
outlined.

MR. HARVEY: Here's a related problem. We intend
through Mr. Stough to also seek to lay a foundation for the
admissibility of letters to the editor and editorials that were
in the Dover papers during the relevant time frame that relate to
this issue and as they are related to the endorsement and the
endorsement issue.

THE COURT: Why can't you recall him for that
purpose? When we see what happens with the reporters why can't
you do that?

MR. ROTHSCHILD: The reporters obviously are not
the author of these letters anyway, so that isn't going to change
with the resolution of the reporters.

MR. WALCZAK: This is a completely non- hearsay
issue that all of these articles are self-authenticating is a
9026 --

MR. WALCZAK: Even those that are coming in not for
the truth of what is said, simply is the fact that this is what's
out there.

THE COURT: Well, I understand that, Mr. Walczak.
But as I just said, I'm not so sure that when you consider the
effect problem it doesn't wash over into the truth. I don't think
it's as pure as you cast it to be. Now, we're talking about
different things. If we're talking about the articles that
contain statements, quotations from individuals school board
members, I think that's entirely problematic, and I don't
necessarily buy into your argument that it self-authenticates for
the purpose of the effect on that.

If we're talking about letters to the editor, I
think that's something different. If we're talking -- it may be
something different. If we're talking about editorials that don't
contain quotes, that may be something different.

MR. GILLEN: I can argue it's not, because the
effect, if that effect is going to be charged to the defendants,
you have to conclude that that's true.

THE COURT: No, I don't know that you do. I think
an editorial is something different and a letter is something
different than an article that contains a quote, particularly a
quote from a school board member on an issue in the case is what
was said during the ramp up to the enactment of the policy.

MR. GILLEN: I understand what you're saying,
Judge, but from our standpoint Steve Stough, he's going to
testify about what he thought when he read a letter to the
editor. That's evidence of the effect of a letter to the editor.
But just as you said, in order to get that effect and charge it
to the defendants, you have to conclude that that letter to the
editor is true. Otherwise --

THE COURT: I don't think you do. No, I disagree
with that, and I'll hear you further on that. I'm not preventing,
my purpose is not to get off the exit ramp here and do an
argument that we don't need to get into.

THE COURT: I understand your argument. I'm not
sure that I yet understand your argument, and we'll pursue that
further, except that I will tell you preliminarily I might view
the letters and editorial as different from the news articles for
the reasons I stated. I think you see where I'm going. You really
need to be prepared to address that as we reconvene this
afternoon with that particular witness. But, you know, to revisit
and put a final point, or a finer point on it as it relates to
the articles themselves, I would likely sustain an objection as
it relates to the articles even on the effect, that's what we're
having the reporters come in for this afternoon. We're going to
have to see how that plays out.

THE COURT: I think the residual, I said this
yesterday, I believe this today, the residual exception under 807
entails fairness to them, you know, if they have the opportunity
to have it at these reporters, and if you're going to introduce
them --

MR. HARVEY: Your Honor, we may do this to preserve
our record today, or we may decide to call them another day after
some of these issues have been cleared up a little bit. Let me
talk to my counsel about that.

THE COURT: But what we have to determine this
afternoon as it relates to Mr. Benn if he comes in here is are
these reporters in the dock on somebody's request that they be
held in contempt. Now, in the first instance it would be you, but
I intend to have a colloquy with the reporters if necessary and
ask them if they're prepared to testify, and that assumes that
you're going to call them to testify. I don't know what you want
to do with that. It seems to me that you ought to do that. I
can't run your case for you, but to --

THE COURT: -- put the onus on the defendants only
and then you say well, we don't know what we're going to do and
they escape the blade from your standpoint, plus if it goes up to
the Third Circuit, and I don't know that there's a distinction,
but if it goes up to the Third Circuit in depositions only and
doesn't go up to the Third Circuit on the testimony of their case
in chief, I think that's a very incomplete issue for the Third
Circuit to rule on.

I might consider wrapping it up and putting a
ribbon on it and sending it out and we'll see what the Third
Circuit says at that point. Of course you could otherwise turn, I
noted that this morning the lazy lawyers, I don't know if that
was directed at the plaintiffs or the defendants in the York
Daily Record, would not establish in your case, I would not use
that for any of you. Did you see that? The York Daily Record put
out a statement indicating that there were lazy lawyers in this
case because you were attempting to subpoena the reporters.

THE COURT: All right. The conversation at side bar
I'll note for the members of the public and the press and the
parties had to do with scheduling, and we have this procedure
that we have agreed on, that we're going to recess at this point
for lunch. As has been noted we have an issue that relates to the
testimony of two witnesses on behalf of the, called by the
plaintiffs.

The testimony would be on behalf of the
plaintiffs. We must resolve that preliminarily this afternoon. I
will meet with counsel in chambers at 1:15 this afternoon in
furtherance of at least attempting to resolve that issue. We'll
not spend an extended period of time doing that, but it could
take a while. I would say that we will go, we will come back into
session likely at approximately 1:45 this afternoon. But that's
an estimate.

I would say anywhere after 1:30 likely we would
reconvene for the afternoon session, and we will resolve at least
temporarily if not permanently the issue of the two witnesses,
and then we will proceed with the balance of the, not the balance
of but the next witness on behalf of the plaintiffs this
afternoon after that matter is dealt with. Anything else from
counsel before we break?